I actually found Talia on Batman: TAS sympathetic as a character, at least to an extent. I also felt sympathy for the Digimon Kaiser, though the series' poorly written plot twists post that ruined it - I was bsaically feeling sympathetic for nothing.
Likewise, on X-Men: TAS I felt horrible for Evil Morph - he was just tortured, depressed and uncertain.
And I gotta love Hank Scorpio - he's a villain, but he just wants what's best for his employees. I love his line - Homer's come to explain that his family's not happy, in the middle of a massive raid. In turn, Hank's line: "Homer, I'm disappointed, but I want what's best for you."
Being that I actually find Naruto's villains more interesting than the main characters, I actually felt sympathy for Itachi when he was
[SPOILER]killed by Sasuke [/SPOILER]
By contrast, I have absolutely no sympathy whatsoever for Mayuri Kurotsuchi.